def __init__(self, search_term, search_operator=None, dataset=None):
self.search_term = search_term
# Make sure search_operator is something we expect
assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
self.search_operator = search_operator
self.dataset = dataset
if self.dataset:
logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
logger.debug("self.dataset.group is: ", pf(self.dataset.group))
# Get group information for dataset and the species id
self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def __init__(self, search_term, search_operator=None, dataset=None):
self.search_term = search_term
# Make sure search_operator is something we expect
assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
self.search_operator = search_operator
self.dataset = dataset
if self.dataset:
logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
logger.debug("self.dataset.group is: ", pf(self.dataset.group))
#Get group information for dataset and the species id
self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def retrieve_sample_data(self, trait):
query = """
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoFreeze.Name = %s AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
"""
logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
return results
def retrieve_sample_data(self, trait):
query = """
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoFreeze.Name = %s AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
"""
logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
return results
